update example data (#88)

* swapped data

* renamed folder

* update metadata files

* remove /data from gitignore

* remove example_data from .docker_ignore

* updated 3D metadata

.dockerignore

@@ -17,7 +17,6 @@ Dockerfile
 
 ## data files## 
 data/
-example_data/
 
 ### Python ###
 # Byte-compiled / optimized / DLL files

.gitignore

@@ -1,4 +1,4 @@
-/data
+
 .DS_Store
 ._*
 # Byte-compiled / optimized / DLL files

data/raw_data/dynamic/2d/fluo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/metadata

@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "HEK293"],
+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
+		}
+	],
+	"EXP_ID" : ["journal_pcbi_1005177"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Ti-E",
+		"CAMERA" : "Andor Neo 5.5",
+		"MAGNIFICATION" : "20x",
+		"NA": "",
+		"BINNING" : "2x2",
+		"PIXEL_SIZE" : "0.65um",
+		"EXPOSURE_TIME" : "",
+		"TIME_STEP" : ""
+		}
+	],
+		"DIMENSIONS" : [{
+		"X" : "1280",
+		"Y" : "1080"
+		}
+	],
+	"ONTOLOGY" : ["dynamic","2d","fluorescence","nuclear"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}

data/raw_data/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/metadata

@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "A549"],
+	"CHANNEL_MARKER" : [{
+		"0" : "Hoescht33342"
+		}
+	],
+	"EXP_ID" : ["20190514_EP01"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "Caltech",
+		"COLLECTED_BY" : "Edward Pao",
+		"DATE_COLLECTED" : "05_14_2019",
+		"DOI" : ""
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Eclipse Ti-2",
+		"CAMERA" : "Prime 95B",
+		"MAGNIFICATION" : "20x",
+		"NA": "0.45",
+		"BINNING" : "1x1",
+		"PIXEL_SIZE" : "0.55um",
+		"EXPOSURE_TIME" : "25ms"
+		}
+	],
+
+		"DIMENSIONS" : [{
+		"X" : "1608",
+		"Y" : "1608"
+		}
+	],
+	"ONTOLOGY" : ["static","2d","fluorescence", "nuclear"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}

data/raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/metadata

@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "DCIS"],
+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
+		}
+	],
+	"EXP_ID" : ["20200116_DCIS"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Ti-E",
+		"CAMERA" : "Andor Neo 5.5",
+		"MAGNIFICATION" : "20x",
+		"NA": "",
+		"BINNING" : "2x2",
+		"PIXEL_SIZE" : "0.65um",
+		"EXPOSURE_TIME" : "",
+		"TIME_STEP" : ""
+		}
+	],
+		"DIMENSIONS" : [{
+		"X" : "512",
+		"Y" : "512"
+		}
+	],
+	"ONTOLOGY" : ["static","2d","mibi","nuclear"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}

data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/metadata

@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "DCIS"],
+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
+		}
+	],
+	"EXP_ID" : ["20200116_DCIS"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Ti-E",
+		"CAMERA" : "Andor Neo 5.5",
+		"MAGNIFICATION" : "20x",
+		"NA": "",
+		"BINNING" : "2x2",
+		"PIXEL_SIZE" : "0.65um",
+		"EXPOSURE_TIME" : "",
+		"TIME_STEP" : ""
+		}
+	],
+		"DIMENSIONS" : [{
+		"X" : "512",
+		"Y" : "512"
+		}
+	],
+	"ONTOLOGY" : ["static","2d","mibi","nuclear"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}

data/raw_data/static/3d/Phase/A549/20190514_EP01/metadata

@@ -0,0 +1,40 @@
+{
+	"TYPE" : ["cell", "A549"],
+	"CHANNEL_MARKER" : [{
+		"0" : "Phase"
+		}
+	],
+	"EXP_ID" : ["20190514_EP01"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "Caltech",
+		"COLLECTED_BY" : "Edward Pao",
+		"DATE_COLLECTED" : "05_14_2019",
+		"DOI" : ""
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Eclipse Ti-2",
+		"CAMERA" : "Prime 95B",
+		"MAGNIFICATION" : "20x",
+		"NA": "0.45",
+		"BINNING" : "1x1",
+		"PIXEL_SIZE" : "0.55um",
+		"EXPOSURE_TIME" : "25ms",
+		"SLICE_SIZE" : "0.25um"
+		}
+	],
+
+		"DIMENSIONS" : [{
+		"X" : "1608",
+		"Y" : "1608"
+		}
+	],
+	"ONTOLOGY" : ["static","2d","Phase"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}